title: MM_0021_B

description: Newly diagnosed patients

source_name: MM_0021_B Bone marrow


title: MM_0020_B

status: Public on Aug 05 2008

type: RNA

city: Saint Herblain

first: Wilfried

last: Gouraud

address: bd Jacques Monod

department: Integrated Center of Oncology René Gauducheau

country: France

institute: ICO (Integrated Center of Oncology Nantes)

description: Newly diagnosed patients

hyb_protocol: Labelled cDNAs were then hybridized in 0.3 ml hybridization mix in scintillation vials for 48 h at 68° C. After hybridization filters were washed twice in 0.1x SSC, 0.1% SDS at 68° C for 90 min.

scan_protocol: DNA microarrays were scanned at 25-µm resolution using a Fuji BAS 5000 image plate system (Raytest, Paris, France). The hybridization signals were quantified using ArrayGauge software v.1.3 (Fuji, Ltd, Tokyo, Japan).

data_processing: For each membrane, the data were normalized by the global intensity hybridization. A background value was calculated from negative controls median ± 6 SD and subtracted to each value. After expression data correction for the amount of PCR product spotted onto the membrane, only features detected in at least 5% of the patients were retained for subsequent analysis. Finally, values are log2-transformed. Data have been normalized with an expression data correction by the amount of PCR product spotted onto the membrane (ratio : Patient probe / Testing probe).

molecule: total RNA

organism: Homo sapiens

source_name: MM_0020_B Bone marrow

label_protocol: Between 0.4 and one µg of total RNA was used as template to generate cDNA bearing T7 promoter, then antisense RNA (aRNA) was generated by in vitro transcription using MEGAscript technology according to the Ambion protocol (Ambion Inc., Austin TX). An aliquot of 2µg of labelled aRNA was then primed with random hexaprimers and reverse transcribed with a mix of cold dNTPs and [a-33P]dCTP.

extract_protocol: Mononuclear bone marrow cells were separated using gradient density centrifugation (lymphocyte separation medium, Eurobio, Les Ulis, France), and plasmacytosis was evaluated by morphology in these mononuclear cell suspensions. Plasma cells (PCs) were then positively selected using anti-CD138–coated microbeads (Miltenyi, Paris, France), because CD138 is expressed only on PCs (normal and malignant) within the bone marrow. Purity and viability of the positively selected cell suspension was assessed by morphology and was above 96% in all the cases. One million PCs were used to prepare total RNA using the guanidinium thiocyanate–phenol method. The RNA integrity was randomly verified by using an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

tag: Tumor

value: multiple myeloma. Tissue:bone marrow. Cells:purified CD138+ plasma cells.


title: brain_old_APB_1

city: Urbana

first: Kelly

middle: Scott

last: Swanson

state: IL

address: 1207 W. Gregory Dr.

country: USA

institute: University of Illinois

description:
339_E.CEL
Gene expression data from cerebral cortex of 12 yr-old dogs after 1 yr on APB diet

hyb_protocol: Purified, fragmented cRNA was hybridized to Affymetrix's Canine Genome Array (version 1) using Affymetrix's GeneChip Fluidics Station 450, as per Affymetrix's instructions.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner 3000

data_processing: Pre-processing was done using the GCRMA algorithm in R and Bioconductor packages. Additionally, Affymetrix's Call Detection algorithm was used to exclude probesets that were not called Present on at least one array or Marginal on two arrays from differential analysis.

label: biotin

organism: Canis lupus familiaris

source_name: Cerebral cortex at 12 yrs, after 1 year on APB diet

label_protocol: Biotin-labeled cRNA samples were made using Affymetrix GeneChip  Expression 3'-Amplification Reagents (One-Cycle Target Labeling and Control Reagents package) according to the manufacturer's instructions.

growth_protocol: Young dogs (mean age = 8 wk at baseline) were fed ad libitum throughout the study to allow for adequate growth; old dogs (mean age = 11.1 yr at baseline) were fed to maintain baseline BW.

extract_protocol: Total RNA was extracted using Trizol as suggested by the manufacturer.

treatment_protocol: Dogs were allotted to 1 of 2 diets and fed for 12 months: 1) animal-protein based (APB) diet primarily composed of highly digestible, animal-derived ingredients and formulated to exceed protein and fat recommendations provided by the Association of American Feed Control Officials (AAFCO) for growth and reproduction; or 2) plant-protein based (PPB) diet primarily composed of moderately digestible, plant-derived ingredients and formulated to meet protein and fat recommendations for growth and reproduction by AAFCO.  The exception was 10% meat and bone meal in the diet.  All samples were collected after an overnight food-restricted period.

tag: Tissue

value: Brain; cerebral cortex

tag: Age

value: 12 yrs

tag: Diet

value: Animal-Protein Based

tag: Breed

value: Beagle


title: brain_old_APB_2

description:
341_E.CEL
Gene expression data from cerebral cortex of 12 yr-old dogs after 1 yr on APB diet


title: Transection day 10 control

city: Bethesda

first: Joe

middle: A

last: Nielsen

state: MD

address: 49 Convent Drive BD49,5A75

institute: NIH/NINDS

hyb_protocol: The fragmented cRNA sample was hybridized to Affymetrix rat U34A microarray for 16 hours at 60rpm at 45Â°C. The microarrays were then washed and stained on the Affymetrix Fluidics Station 400 using instructions and reagents purchased from Affymetrix.

scan_protocol: Scanning was performed with a Hewlett-Packard G2500A Gene Array Scanner.

data_processing: Probe-level summarization was accomplished using the Affymetrix MAS 5.0 Algorithm. Resulting expression data was log (base=2) transformed and quantile normalized using R (bioconductor). Expression data construed as noise by Affymetrix Control Fragment modeling (Coeficient of Variation ~ expression) were floored to 6.35. While, four additional expression measurements for each gene fragment for each corresponding microarray were created using the model in conjunction with the random normal distribution. Per gene fragment selection, analysis of variance (i.e., ANOVA) was used in conjunction with a minimum effect difference filter. Such that, gene fragments having a Bonferroni family-wise error multiple comparison corrected p-value < 0.05 and a 2-fold minimum effect difference were kept for use in Temporal clustering analysis.

organism: Rattus norvegicus

source_name: pontine nuclei transection day10 control

label_protocol: Seven micrograms from each total RNA sample was converted into double-stranded cDNA by using SuperScript choice system with an oligo-dT primer containing T7 RNA polymerase promoter. The double-stranded cDNA was purified by phenol/chloroform extraction and then used for in vitro transcription using ENZO BioArray RNA transcript labelling kit.  Biotin-labelled cRNA was purified with the RNeasy kit and fragmented to approximately 200bp.

extract_protocol: Trizol reagent

tag: adult male Sprague-Dawley rats


title: Transection day 37 control

source_name: pontine nuclei transection day37 control


title: MM_0019_B

description: Newly diagnosed patients

source_name: MM_0019_B Bone marrow


title: Transection day 10 lesion

source_name: pontine nuclei transection day10 lesion


title: brain_old_PPB_1

description:
340_E.CEL
Gene expression data from cerebral cortex of 12 yr-old dogs after 1 yr on PPB diet

source_name: Cerebral cortex at 12 yrs, after 1 year on PPB diet

value: Plant-Protein Based


title: Lysolecithin day 37 lesion

source_name: pontine nuclei lysolecithin day37 lesion


title: Lysolecithin day 37 control

source_name: pontine nuclei lysolecithin day37 control


title: MM_0015_B

description: Newly diagnosed patients

source_name: MM_0015_B Bone marrow


title: MM_0018_B

description: Newly diagnosed patients

source_name: MM_0018_B Bone marrow


title: Lysolecithin day 10 lesion

source_name: pontine nuclei lysolecithin day10 lesion


title: MM_0012_B

description: Newly diagnosed patients

source_name: MM_0012_B Bone marrow


title: MM_0016_B

description: Newly diagnosed patients

source_name: MM_0016_B Bone marrow


title: MM_0014_B

description: Newly diagnosed patients

source_name: MM_0014_B Bone marrow


title: MM_0011_B

description: Newly diagnosed patients

source_name: MM_0011_B Bone marrow


title: MM_0017_B

description: Newly diagnosed patients

source_name: MM_0017_B Bone marrow


title: MM_0009_B

description: Newly diagnosed patients

source_name: MM_0009_B Bone marrow


title: Saline day 37 lesion

source_name: pontine nuclei saline day37 lesion


title: Lysolecithin day 10 control

source_name: pontine nuclei lysolecithin day10 control


title: Lysolecithin day 4 lesion

source_name: pontine nuclei lysolecithin day4 lesion


title: MM_0013_B

description: Newly diagnosed patients

source_name: MM_0013_B Bone marrow


title: DHT: Time:12h

city: Quebec

first: Ezequiel

middle: L

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

country: Canada

institute: CRCHUL

description: Analysis of uteri of 10-11 weeks old C57Bl/6 females sacrified 12h after a single injection of  0.1mg/mouse of Dihydrotestosterone (DHT).

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip MOE 430 2.0 Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000 G7.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: Biotin

organism: Mus musculus

source_name: Uteri of 10-11 weeks old C57Bl/6 females sacrified 12h after a single injection of 0.1mg/muose of Dihydrotestosterone (DHT).

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 20 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Ten to eleven week-old female C57BL6 mice were received from Charles River (St Constant, Canada) and were allowed to acclimate for 4 weeks. The animals were housed individually in an environmentally-controlled room (temperature: 22 ± 3°C; humidity: 50 ± 20%; 12-h light-12-h dark cycles, lights on at 07:15h). The mice had free access to tap water and a certified rodent feed (Lab Diet 5002 (pellet), Ralston Purina, St Louis, MO).

extract_protocol: Mice were anesthetized by inhalation of isoflurane and exsanguinated via cardiac puncture followed by cervical dislocation. Then, total uterus was collected and any adhering tissue was removed. Tissue was then rapidly frozen in liquid nitrogen and kept at -80C until RNA extraction. Trizol extraction of total RNA was performed from pooled tissues, according to the manufacturer's instructions (Invitrogen).

treatment_protocol: Ten 10-11 weeks old C57Bl/6 mice were gonadectomized under isoflurane-induced anesthesia and sacrified seven days after GDX.  Mice  were injected s.c with DHT (0.1mg/mice) or vehicle, at 0.5, 1, 3, 6, 12 or 24h before sacrifice. Uteri was removed and pooled before total RNA extraction.

tag: Genotype C57BL6

value: 10-11 weeks old


title: MM_0006_B

description: Newly diagnosed patients

source_name: MM_0006_B Bone marrow


title: MM_0007_B

description: Newly diagnosed patients

source_name: MM_0007_B Bone marrow


title: MM_0008_B

description: Newly diagnosed patients

source_name: MM_0008_B Bone marrow


title: DHT: Time:3h

description: Analysis of uteri of 10-11 weeks old C57Bl/6 females sacrified 3h after a single injection of  0.1mg/mouse of Dihydrotestosterone (DHT).

source_name: Uteri of 10-11 weeks old C57Bl/6 females sacrified 3h after a single injection of 0.1mg/mouse of Dihydrotestosterone (DHT).


title: MM_0010_B

description: Newly diagnosed patients

source_name: MM_0010_B Bone marrow


title: MM_0005_B

description: Newly diagnosed patients

source_name: MM_0005_B Bone marrow


title: Saline day 10 lesion

source_name: pontine nuclei saline day10 lesion


title: Saline day 37 control

source_name: pontine nuclei  saline day37 control


title: DHT: Time:24h

description: Analysis of uteri of 10-11 weeks old C57Bl/6 females sacrified 24h after a single injection of  0.1mg/mouse of Dihydrotestosterone (DHT).

source_name: Uteri of 10-11 weeks old C57Bl/6 females sacrified 24h after a single injection of 0.1mg/mouse of Dihydrotestosterone (DHT).


title: DHT: Time:1h

description: Analysis of uteri of 10-11 weeks old C57Bl/6 females sacrified 1h after a single injection of  0.1mg/mouse of Dihydrotestosterone (DHT).

source_name: Uteri of 10-11 weeks old C57Bl/6 females sacrified 1h after a single injection of 0.1mg/mouse of Dihydrotestosterone (DHT).


title: MM_0004_B

description: Newly diagnosed patients

source_name: MM_0004_B Bone marrow


title: Saline day 4 lesion

source_name: pontine nuclei saline day4 lesion


title: DHT: Time:18h

description: Analysis of uteri of 10-11 weeks old C57Bl/6 females sacrified 18h after a single injection of  0.1mg/mouse of Dihydrotestosterone (DHT).

source_name: Uteri of 10-11 weeks old C57Bl/6 females sacrified 18h after a single injection of 0.1mg/mouse of Dihydrotestosterone (DHT).


title: DHT: Time:6h

description: Analysis of uteri of 10-11 weeks old C57Bl/6 females sacrified 6h after a single injection of  0.1mg/mouse of Dihydrotestosterone (DHT).

source_name: Uteri of 10-11 weeks old C57Bl/6 females sacrified 6h after a single injection of 0.1mg/mouse of Dihydrotestosterone (DHT).


title: MM_0001_B

description: Newly diagnosed patients

source_name: MM_0001_B Bone marrow


title: MM_0003_B

description: Newly diagnosed patients

source_name: MM_0003_B Bone marrow


title: MM_0002_B

description: Newly diagnosed patients

source_name: MM_0002_B Bone marrow


title: Saline day 10 control

source_name: pontine nuclei saline day10 control


title: DHT: Time:0h

description: Analysis of uteri of 10-11 weeks old C57Bl/6 females sacrified 24h after a single injection of vehicle (Control animal).

source_name: Uteri of 10-11 weeks old C57Bl/6 females sacrified 24h after a single injection of vehicle.

treatment_protocol: Ten 10-11 weeks old C57BL6 mice were ovariectomized under isoflurane-induced anesthesia and sacrified seven days after GDX.  24h before sacrifice, mice  were injected s.c vehicle solution (Control group).


title: Control

source_name: pontine nuclei healthy control

tag: adult male sprague dawley rat


title: Terbutyl stress TR t16 replicate 3

status: Public on May 23 2008

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

description:
After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for various times.
Filters were stripped by washing them once with 50 mM NaOH at 45ºC, once with 50 mM Tris-HCl, pH 7.5, 0.1x SSC, 0.1% SDS and once pouring with boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane and left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked with a Geiger counter or re-scanned with the Phosphorimager.

hyb_protocol: Hybridization Solution was: 5XSSC, 5XDenhart’s, 0.5% SDS and 100 µg herring sperm DNA/ml. The hybridization protocol used was as follows. Filters were inserted in 12.5X2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 5 ml of the same solution containing 3X10exp6 dpm/mL of radioactive sample and hybridized for 44h. Washing conditions were: 1h at 65ºC for 20 min in 2XSSC, 0.1% SDS, and twice at 65ºC for 30 min in 0.2XSSC, 0.1% SDS.

scan_protocol: Images were acquired using a FujiFilm FLA3000 Phosphorimager.

data_processing: Raw image quantization background subtracted.

organism: Saccharomyces cerevisiae

source_name: W303-1a strain replicate 3 growing in exponential phase

label_protocol:
In vivo labeling by run-on (GRO) using 33P-UTP.
Around 6 x 10exp8 yeast cells were used to perform in vivo transcription. After spinning down cells, they were washed in cold water and the cell pellet was resuspended in 900 µl of sterile cold water (final volume 950 µl). Then, the cell suspension was transferred to a fresh micro centrifuge tube, 50 µl of 10% sarkosyl were added and cells were incubated for 20 minutes on ice. After the permeabilization step, cells were recovered by low-speed centrifugation and the supernatant was removed. In vivo transcription was performed by resuspending cells in 120 µl of 2.5x transcription buffer (50 mM Tris-HCl pH 7.7, 500 mM KCl, 80 mM MgCl2), 16 µl of AGC mix (10 mM each of CTP, ATP and GTP), 6 µl of DTT (0.1 M) and 13 µl of [α-33P]UTP (3000 Ci/mmol, 10 μCi/µL). Cells were maintained on ice at all times. The final volume was adjusted to 300 µl with distilled water and the mix was incubated for 5 minutes at 30ºC to allow transcription elongation. The reaction was stopped by adding 1 ml of cold distilled water to the mix.

extract_protocol:
Total RNA isolated from yeast cells was prepared as described by Sherman et al. [1986], but using a multiple-sample automated device (Fast-Prep, BIO101) to break the cells.
Sherman F, Fink GR, Hicks JB (1986) Methods in yeast genetics.
Spring Harbor Cold Laboratory Press, Cold Spring Harbor, New York

treatment_protocol:
Oxidative stress conditions were created by addition of t-butyl hydroperoxide (t-BOOH) at 0.1 mM. Experiments were initiated on exponential cultures that had been grown in such conditions for at least ten generations, at concentrations of 1.5-2 x 10exp7 cells/ml.
t16: 16 minutes after adding t-butyl.

tag: In vivo labeled total RNA from W303-1a yeast strain.

value: 16 minutes after adding terbutyl.

tag: Hybridization on macrochip F9.


title: Transcriptome of B cells

status: Public on Jul 03 2008

city: Berlin

first: Marc

last: Sultan

address: Ihnestr. 73

country: Germany

institute: Max Planck Institute for molecular genetics

description:
cRNA samples were hybridized as biological and technical duplicates on Illumina HumanRef8 V2.0 BeadChips.

B1-1raw.txt: 	B cell biological replicate 1, 	technical replicate 1
B1-2raw.txt: 	B cell biological replicate 1, 	technical replicate 2
B2-1raw.txt: 	B cell biological replicate 2, 	technical replicate 1
B2-2raw.txt: 	B cell biological replicate 2, 	technical replicate 2

hyb_protocol: Chip hybridisations, washing and Cy3-streptavidin (Amersham Biosciences) staining were performed on the Illumina BeadStation 500 platform employing reagents and following protocols supplied by the manufacturer.

scan_protocol: scanning was performed on the Illumina BeadStation 500 platform

data_processing: Raw expression data (BeadSummary gene profile files), without normalization, were extracted from the manufacturer’s Illumina BeadStudio application software 1.0. Further processing of the data was done within the R / Bioconductor statistical analysis software package. We calculated the Pearsons product moment correlation coefficient on the non-normalized data sets to remove outliers and to check for integrity of the experiments (r>=0.98), followed by the computation of intra-chip pair-wise scatter-plots for each probe. The raw data sets were then normalized using quantile normalization.

source_name: ramos B cells

label_protocol: Biotin-labelled cRNA was generated using a linear amplification kit (Ambion #IL1791) starting with 500 ng of DNA-free, quality-checked total RNA of each sample as input (see RNA preparation).

growth_protocol: B cells were cultured parallely in 2*150 cm3 flasks with RPMI 1640 (penicillin-streptomycin) (Gibco) supplemented with 10% FCS (Biochrom) and Glutamax (1x) (Gibco). At passage 20 (confluent state), cells were  trypsinized, washed off in PBS, pelleted, and resuspended in 2 ml lysis solution RLT (Qiagen).

extract_protocol:
RNA preparation and double stranded cDNA generation
Total RNA was then extracted from ~ 20 x 106 cells per sample (2*HEK and 2*B cells samples) using RNeasy Midi extraction kit (Qiagen) by following the manufacturer’s instructions. DNA was removed using the “on column digestion” protocol of the RNeasy Midi extraction kit (Qiagen).  Total RNA quality was assessed by spectrophotometry (Nanodrop) and gel electrophoresis (1% agarose).

tag: Ramos B cell line


title: Terbutyl stress TR t41 replicate 3

treatment_protocol:
Oxidative stress conditions were created by addition of t-butyl hydroperoxide (t-BOOH) at 0.1 mM. Experiments were initiated on exponential cultures that had been grown in such conditions for at least ten generations, at concentrations of 1.5-2 x 10exp7 cells/ml.
t41: 41 minutes after adding t-butyl.

value: 41 minutes after adding terbutyl.

tag: Hybridization on macrochip F5.


title: Ex-smoker, Normal B10 (smoke)

status: Public on Oct 01 2008

city: Groningen

first: Mirjam

last: Boelens

address: Hanzeplein 1

country: Netherlands

institute: UMCG

hyb_protocol: Hybridization was performed with 750 ng of each labeled target together with fragmentation- and hybridization buffer at 60C for 17 hours onto Agilent Whole Human Genome oligoarrays following manufacturer’s protocol.

scan_protocol: The microarray slides were washed following the user manual instructions and scanned using the Agilent dual laser DNA microarray scanner. The microarray data were normalized using the Agilent feature extraction software v. 8.5 (Agilent Technologies, Palo Alto, CA) with regards to no background correction.

data_processing: Quantile normalization was applied to log2 transformed median signals of Cy5 and Cy3 intensities. Principal component analysis was performed and samples with a factor loading with a first principal component of more than two times the standard deviation from the mean were excluded as their hybridisations were considered to be of low quality. Intensities were standardised by subtracting the variance explained by the first principal component, as this is gene specific variation that does not contribute to differences between arrays. Probe sequences that were spotted more than once were averaged. For every sample, datasets of Cy3 and Cy5 were averaged.

label: Cy3 and Cy5

source_name: B10, ex-smoker

label_protocol:
ULS LABELING
1. Take 1- 2 μg of aRNA. Ensure that the final concentration in the labeling reaction is above 50 ng/μL. Optimal modification degrees of the labeled material are not achieved if the final concentration of aRNA in the labeling mixture is below 50 ng/μL)
2. Add 1 μL of Cy5-ULS or Cy3-ULS per 1 μg aRNA (Always keep the ratio of μg of aRNA to μL ULS 1:1 when increasing or decreasing the amount to be labeled).
3. Add 1/10 volume of 10 x Labeling solution
4. Adjust with RNase-free water to final volume and mix by pipetting
5. Label sample by incubation for 15 minutes at 85°C
6. Place samples on ice, spin down to collect contents of tube before proceeding with purification using the KREApure columns
Dye Removal using KREApure Columns (Removal of free ULS label using KREApure columns
(20800 x g is equivalent to 14,000 rpm on eppendorf 5417C)):
1. Resuspend column material by vortexing
2. Loosen cap ¼ turn and snap off the bottom closure
3. Place the column in a 2 mL collection tube
4. Pre-spin the column for 1 minute at 20800 x g
5. Discard flow through and column cap, but re-use collection tube
6. Add 300 μL ultrapure water to the column and centrifuge for 1 min at 20,800g
7. Discard collection tube and flow-through
8. Place column in a new RNase free 1.5 mL microcentrifuge tube (not provided)
9. Add ULS-labeled aRNA onto column bed
10. Centrifuge column for 1 minute at 20800 x g
11. Flow through contains the purified labeled aRNA

extract_protocol:
LASER DISSECTION MICROSCOPY
- Frozen bronchial wall of 8μm were used for laser dissection microscopy (LDM)
- Only histologically normal bronchial epithelial cells were isolated using laser dissection microscopy
- An area of approximately 25x106 μm2 was microdissected from the section using P.A.L.M. Microlaser Technology system (P.A.L.M., Bernried, Germany).
- Laser microdissected cells were collected in lysis buffer (Macherey-Nagel)
RNA ISOLATION
Total RNA was isolated and purified from the microdissected cells with a Nucleospin RNA II kit (Macherey-Nagel). The quantity of DNA-free total RNA was measured using a Nanodrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). RNA quality was assessed by the presence and ratio of 18S and 28S rRNA bands combined with a low baseline, monitored with RNA 6000 PicoChip (Agilent, Palo Alto, CA) on the 2100 bioanalyzer (Agilent).
RNA AMPLIFICATION
For each sample, 150 ng total RNA was amplified using the MessageAmp II kit (Ambion, Austin, USA). Briefly, 150 ng total RNA was mixed with 1 l of T7 Oligo(dT) primer in a total volume of 12 l. Primer and template were denatured by incubating at 70C for 10 minutes and annealed by putting the reaction tubes on ice. The First Strand Reaction was performed by adding 8 µl Reverse Transcription Master Mix (containing 10x First Strand buffer, Ribonuclease Inhibitor, dNTP Mix and Reverse Transcriptase) and incubating at 42C for 2 hours. Second Strand cDNA Synthesis was done by adding 63 µl Nuclease-Free Water, 10 µl 10x Second Strand Buffer, 4µl dNTP Mix, 2µl DNA Polymerase and 1 µl RNase H and incubating at 16C for 2 hours. cDNA purification was done according manufacturers protocol (Ambion). In vitro transcription was initiated by addition of 2 µl aaUTP Solution (50mM), 12 µl ATP, CTP, GTP mix (25mM), 3 µl UTP Solution (50mM), 4 µl T7 10x Reaction Buffer and 4 µl T7 Enzyme Mix and incubated at 37C for 9 hours. Machery-Nagel RNA Clean up mini spin columns are used for purification of the cRNA.

tag: Sample code

tag: Cell type:			histologically normal bronchial epithelial cells that were laser microdissected from frozen bronchial wall tissue

tag: Gender

value: male

tag: Age at time of surgery:	74

tag: Smoking status:		ex

tag: Packyears:			45

tag: Surgery due to:		squamous cell carcinoma

tag: Type of Surgery:		lobectomy

tag: Location tumor:		left lower lobe

tag: TNM stage:			T2N1M0

tag: COPD:				no COPD

tag: FEV1/FVC:			72 %

tag: GOLD stage:			not applicable


title: Terbutyl stress TR t71 replicate 3

treatment_protocol:
Oxidative stress conditions were created by addition of t-butyl hydroperoxide (t-BOOH) at 0.1 mM. Experiments were initiated on exponential cultures that had been grown in such conditions for at least ten generations, at concentrations of 1.5-2 x 10exp7 cells/ml.
t71: 71 minutes after adding t-butyl.

tag: In vivo labeled total RNA from W303-1a yeast strain.

value: 71 minutes after adding terbutyl.

tag: Hybridization on macrochip F6.


title: Transcriptome of HEK293T cells

description:
cRNA samples were hybridized as biological and technical duplicates on Illumina HumanRef8 V2.0 BeadChips.

HEK2-1raw.txt: 	HEK biological replicate 1, 	technical replicate 1
HEK2-2raw.txt: 	HEK biological replicate 1,	technical replicate 2
HEK4-1raw.txt: 	HEK biological replicate 2, 	technical replicate 1
HEK4-2raw.txt: 	HEK biological replicate 2, 	technical replicate 2

hyb_protocol: Chip hybridisations, washing, and Cy3-streptavidin (Amersham Biosciences) staining were performed on the Illumina BeadStation 500 platform employing reagents and following protocols supplied by the manufacturer. cRNA samples were hybridized as biological and technical duplicates on Illumina HumanRef8 V2.0 BeadChips.

source_name: HEK293T cells

label_protocol: Biotin-labelled cRNA was generated using a linear amplification kit (Ambion #IL1791) starting with 500 ng of DNA-free, quality-checked total RNA of each sample as input (see RNA preparation)

growth_protocol: HEK 293T cells were cultured in parallel in 2*150 cm3 flasks with DMEM (penicillin-streptomycin) (Gibco) supplemented with 10% Fetal Calf Serum (FCS) (Biochrom) and Glutamax (1x) (Gibco). At passage 20 (confluent state), cells were  trypsinized, washed off in PBS, pelleted and resuspended in 2 ml lysis solution RLT (Qiagen).

extract_protocol: Total RNA was then extracted from ~ 20 x 106 cells per sample (2*HEK and 2*B cells samples) using RNeasy Midi extraction kit (Qiagen) by following the manufacturer’s instructions. DNA was removed using the “on column digestion” protocol of the RNeasy Midi extraction kit (Qiagen).  Total RNA quality was assessed by spectrophotometry (Nanodrop) and gel electrophoresis (1% agarose)

tag: Human embryonic kidney (HEK293T) cells


title: ISE6_3

status: Public on Aug 04 2008

city: St. Paull

first: Michael

last: Herron

state: MN

address: 1980 Folwell Avenue, Room 219 Hodson Hall

department: Entomology

institute: Michael Herron

description: Expression profiling of uninfected tick cell line; control

hyb_protocol: Samples were hybridized to tiling arrays at the BioMedical Genomics Center at the University of Minnesota using the Affymetrix Fluidics Station 400 according to standard Affymetrix protocols

scan_protocol: Arrays were scanned using an Affymetrix Genechip 3000 scanner according to standard Affymetrix protocols

data_processing:
.CEL files generated by the University of Minnesota’s microarray facility were joined to Affymetrix BPMAP files specific to the tiling array using Affymetrix® Tiling Analysis Software (TAS).  TAS generated a list of signal intensities and arranged them in order of genomic location and DNA strand. The intensity values were normalized via quantiles, and imported into the IgorPro data analysis program (WaveMetrics Lake Oswego OR, USA) along with the ORF and structural RNA annotations available from (http://www.ncbi.nlm.nih.gov). A script was written to index a trapezoidal integration algorithm of the intensity list with the start and end genomic positions indicated on the annotation. This script operation generated a list of 1411 “areas under the curve.”
Note, the normalized data contains all of the signal intensities for the Anaplasma sequence but it does not contain control feature intensities because these intensities were never normalized in this analysis.
In addition, the normalized data for the uninfected host cells (HL60, HMEC, ISE6 files) was also baseline adjusted to align the baselines of the independently normalized HzHL60, HzHMEC, and HzISE6 files. Specifically, the signal intensity of these uninfected arrays was baseline adjusted using the signal intensities of twelve manually selected intergenic regions devoid of obvious signal from across the span of the genome.

organism: Ixodes scapularis

source_name: Cell Culture

label_protocol: Total RNA from Ap infected or sterile control cells was processed for Ap transcript measurement according to the Affymetrix “Prokaryotic Target Preparation” protocol using random priming of total RNA to synthesize a single strand of cDNA. The cDNA was recovered by column purification, fragmented with DNase I, and end labeled with biotin. These biotinylated cDNA fragment “targets” were hybridized to the “probes” contained on the tiling arrays, labeled with a streptavidin-phycoerytherin conjugate, and probe hybridization was quantified by laser scanning.

extract_protocol: Ap genomic transcription was measured in each of the three cell lines when cultures were approximately 95% infected. Typically, cells contained hundreds of bacteria. RNA was extracted from three Ap-infected and three uninfected samples of each cell line (18 samples total). Each sample was from a separate culture flask and consisted of 10^7 infected cells or uninfected control cells. Cells were suspended by pipetting (HL-60 and ISE6) or with a cell scraper (HMEC-1) and immediately centrifuged at 300 ´ g for 2 minutes. The supernatant was aspirated and discarded, cell pellets were loosened by flicking and immediately placed in TRI REAGENT™ (Sigma, Saint Louis, MO). All steps were performed at room temperature. Total RNA was then isolated according to the TRI REAGENT™ product instructions. In brief, samples in TRI REAGENT™ were extracted with chloroform and centrifuged at 12,000 x g for 15 minutes at 4 ºC. RNA in the aqueous, upper phase was precipitated in isopropanol, collected by centrifugation at 12,000 x g for 10 minutes at 4 ºC, and washed twice in cold 75% ethanol. RNA pellets were dissolved in 100 µL RNase-free water, quantified by spectrophotometry, and processed for array analysis.

tag: uninfected ISE6 Host Cell


title: ISE6_2


title: HMEC_3

description: Expression profiling of uninfected human cell line; control

tag: uninfected HMEC-1 Host cell


title: Terbutyl stress TR t26 replicate 3

treatment_protocol:
Oxidative stress conditions were created by addition of t-butyl hydroperoxide (t-BOOH) at 0.1 mM. Experiments were initiated on exponential cultures that had been grown in such conditions for at least ten generations, at concentrations of 1.5-2 x 10exp7 cells/ml.
t26: 26 minutes after adding t-butyl.

value: 26 minutes after adding terbutyl.

tag: Hybridization on macrochip F10.


title: Terbutyl stress TR t7 replicate 3

treatment_protocol:
Oxidative stress conditions were created by addition of t-butyl hydroperoxide (t-BOOH) at 0.1 mM. Experiments were initiated on exponential cultures that had been grown in such conditions for at least ten generations, at concentrations of 1.5-2 x 10exp7 cells/ml.
t7: 7 minutes after adding t-butyl.

value: 7 minutes after adding terbutyl.

tag: Hybridization on macrochip F8.


title: Terbutyl stress TR t0 replicate 3

treatment_protocol:
Oxidative stress conditions were created by addition of t-butyl hydroperoxide (t-BOOH) at 0.1 mM. Experiments were initiated on exponential cultures that had been grown in such conditions for at least ten generations, at concentrations of 1.5-2 x 10exp7 cells/ml.
t0: before adding t-butyl.

value: before adding terbutyl.

tag: Hybridization on macrochip F7.


title: HL60_3

tag: uninfected HL60 Host cell


title: Terbutyl stress TR t41 replicate 2

source_name: W303-1a strain replicate 2 growing in exponential phase


title: Terbutyl stress TR t26 replicate 2

tag: Hybridization on macrochip F9.


title: HzISE6_2

description: Expression profiling of Ap Hz-infected tick  cell line

organism:
Ixodes scapularis
Anaplasma phagocytophilum str. HZ

tag: Ap Strain Hz-infected ISE6 Host Cell


title: HzHMEC_2

description: Expression profiling of Ap Hz-infected human cell line

organism:
Homo sapiens
Anaplasma phagocytophilum str. HZ

tag: Ap Strain Hz-infected HMEC-1 Host cell


title: ISE6_1


title: HL60_1


title: HMEC_1


title: HzHL60_2

tag: Ap Strain Hz-infected HL60 Host cell


title: Terbutyl stress TR t16 replicate 2


title: Terbutyl stress TR t7 replicate 2


title: Terbutyl stress TR t71 replicate 1

source_name: W303-1a strain replicate 1 growing in exponential phase


title: Terbutyl stress TR t16 replicate 1


title: Terbutyl stress TR t26 replicate 1


title: HzHL60_3


title: HzHL60_1


title: Terbutyl stress TR t0 replicate 1

tag: Hybridization on macrochip F5.


title: Terbutyl stress TR t7 replicate 1


title: HL60_2


title: HzISE6_3


title: HzHMEC_3


title: HzISE6_1


title: Terbutyl stress TR t0 replicate 2


title: HMEC_2


title: HzHMEC_1


title: Testosterone + tamoxifen T+TAM 6

status: Public on Mar 22 2008

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description: Gene expression data, continuous culture as indicated in 'characteristics'

hyb_protocol: The chips were hybridized by Affymetrix Hybridization Oven 640 and washed by Affymetrix Fluidics Station 450 according to manufacturer's protocols.

scan_protocol: The chips were scanned by Affymetrix scanner 3000 7G using manufacturer's default settings.

data_processing: Raw Affymetrix intensity measurements of all probe sets were background-corrected, normalized, and summarized into gene level expression measurements using RMA method implemented in Partek Genomic Suite V6.0.

source_name: Testosterone + Tamoxifen Resistant, replicate 6

label_protocol: One-Cycle target labeling was performed using 5ug of total RNA according to Affymetrix's Eukaryotic Target Labeling protocol.

growth_protocol: Cells were grown in continuous culture with hormone or inhibitor, depending on the type of resistant cell line indicated above

extract_protocol: TRIzol reagent (Invitrogen, Carlsbad, CA) was used for RNA isolation from cell lines, according to manufacturer’s protocol

treatment_protocol: RNA was harvested from resistant cell lines growing in above-mentioned growth protocol conditions

tag: Testosterone + Tamoxifen


title: Testosterone-free resistant line ANA R 1

source_name: Anastrozole Only resistant, replicate 1

tag: Anastrozole


title: Transection day 4 lesion

source_name: pontine nuclei transection day4 lesion

tag: adult male Sprague-Dawley rats


title: Testosterone + tamoxifen T+TAM 1

source_name: Testosterone + Tamoxifen Resistant, replicate 1


title: Testosterone-free resistant line ANA R 2

source_name: Anastrozole Only resistant, replicate 2


title: Testosterone-free resistant line EXE R 3

source_name: Exemestane Only resistant, replicate 3

tag: Exemestane


title: Testosterone-free resistant line LTEDaro 3

source_name: Long-term estrogen deprived, replicate 3

tag: No hormone, no inhibitor


title: Testosterone-free resistant line ANA R 3

source_name: Anastrozole Only resistant, replicate 3


title: Testosterone + tamoxifen T+TAM 5

source_name: Testosterone + Tamoxifen Resistant, replicate 5


title: Testosterone-free resistant line LTEDaro 1

source_name: Long-term estrogen deprived, replicate 1


title: Testosterone-free resistant line EXE R 1

source_name: Exemestane Only resistant, replicate 1


title: Testosterone + exemestane T+EXE 4

source_name: Testosterone + Exemestane Resistant, replicate 4

tag: Testosterone + Exemestane


title: Testosterone-free resistant line EXE R 2

source_name: Exemestane Only resistant, replicate 2


title: Testosterone-free resistant line LTEDaro 2

source_name: Long-term estrogen deprived, replicate 2


title: Testosterone + tamoxifen T+TAM 4

source_name: Testosterone + Tamoxifen Resistant, replicate 4


title: Testosterone + tamoxifen T+TAM 2

source_name: Testosterone + Tamoxifen Resistant, replicate 2


title: Testosterone + tamoxifen T+TAM 3

source_name: Testosterone + Tamoxifen Resistant, replicate 3


title: Testosterone + exemestane T+EXE 6

source_name: Testosterone + Exemestane Resistant, replicate 6


title: Testosterone + exemestane T+EXE 5

source_name: Testosterone + Exemestane Resistant, replicate 5


title: Testosterone + exemestane T+EXE 2

source_name: Testosterone + Exemestane Resistant, replicate 2


title: Testosterone + anastrozole T+ANA 3

source_name: Testosterone + Anastrozole Resistant, replicate 3

tag: Testosterone + Anastrozole


title: Testosterone + exemestane T+EXE 3

source_name: Testosterone + Exemestane Resistant, replicate 3


title: Testosterone + exemestane T+EXE 1

source_name: Testosterone + Exemestane Resistant, replicate 1


title: Testosterone + anastrozole T+ANA 4

source_name: Testosterone + Anastrozole Resistant, replicate 4


title: Testosterone + anastrozole T+ANA 5

source_name: Testosterone + Anastrozole Resistant, replicate 5


title: Testosterone + anastrozole T+ANA 6

source_name: Testosterone + Anastrozole Resistant, replicate 6


title: Testosterone + anastrozole T+ANA 1

source_name: Testosterone + Anastrozole Resistant, replicate 1


title: Testosterone + anastrozole T+ANA 2

source_name: Testosterone + Anastrozole Resistant, replicate 2


title: Testosterone T-only 6

source_name: Testosterone-Only, replicate 6

tag: Testosterone


title: Testosterone + letrozole T+LET 6

source_name: Testosterone + Letrozole Resistant, replicate 6

tag: Testosterone + Letrozole


title: Testosterone T-only 5

source_name: Testosterone-Only, replicate 5


title: Testosterone + letrozole T+LET 1

source_name: Testosterone + Letrozole Resistant, replicate 1


title: Testosterone T-only 4

source_name: Testosterone-Only, replicate 4


title: Testosterone + letrozole T+LET 4

source_name: Testosterone + Letrozole Resistant, replicate 4


title: Testosterone + letrozole T+LET 3

source_name: Testosterone + Letrozole Resistant, replicate 3


title: Testosterone + letrozole T+LET 5

source_name: Testosterone + Letrozole Resistant, replicate 5


title: MCF-7aro Control 2

source_name: MCF7-aro parental control replicate 2

tag: Control, no hormone, no inhibitor


title: MCF-7aro Control 1

source_name: MCF7-aro parental control replicate 1


title: Testosterone T-only 2

source_name: Testosterone-Only, replicate 2


title: Testosterone T-only 1

source_name: Testosterone-Only, replicate 1


title: Normal control skin epithelium_7

status: Public on Dec 15 2006

city: Vancouver

first: Kevin

last: McElwee

state: BC

department: Dermatology and Skin Science

institute: University of British Columbia

description: All treated biologicaly replicated samples were hybridized with the same universal human reference RNA (reference).

scan_protocol: The two fluorescent images (Cy3 and Cy5) were scanned separately using a Perkin Elmer ScanArray Express Scanner (PerkinElmer Life And Analytical Sciences, Inc., Wellesley, MA).

data_processing: Arrays were scanned at excitation wave lengths of 532 and 635 nm to detect the Cy3 and Cy5 dyes, respectively. Image analysis and quantification were conducted with commercial software, (ImaGene 7.0 software: BioDiscovery Inc., El Segundo, CA, USA). After grid assignment, the adjusted intensity for each gene was calculated by subtracting the background. This value was used as the input for the Genespring 7.2 program (Silicon Genetics, Redwood City, CA, USA).

source_name: normal skin epithelium

label_protocol: 1 ug RNA were amplified using the SenseAmp plus kit (Genisphere Inc, Hatfield, PA). The calculated A 260/280 ratio was used to determine the appropriate amount of sense RNA for labeling. sense RNA from amplification was labeled with Cy5, with the 3DNA array detection 350 kit (Genisphere) and hybridized to cDNA microarrays.

growth_protocol: sample was stored in an RNA stabilization reagent

extract_protocol: Total RNA was isolated with an RNeasy Fibrous Tissue Midi Kit (Qiagen) according to the manufacturer's protocols.The quantity and quality of the RNAs was measured by electrophoresis using the Agilent 2100 bioanalyzer and RNA 6000 nano kit (Agilent Technologies, Palo Alto, CA).

treatment_protocol: sample was collected in the operating theater during Moh’s surgical excision

tag: normal skin epithelium

label_protocol: Total 10ug RNA universal human reference RNA (Stratagene, Cedar Creek, TX) was labeled with Cy3 , with the 3DNA array detection 350 kit (Genisphere) and hybridized to cDNA microarrays.

tag: The Universal Human Reference RNA is composed of total RNA isolated from cell lines representing different human tissues for optimal broad gene coverage.


title: 9a5ccy3 x Fb7cy5-Replica 2

status: Public on Jul 18 2007

type: genomic

city: Santo André

first: Luiz

middle: R.

last: Nunes

state: SP

address: Rua Santa Adélia 166

department: Centro de Ciências Naturais e Humanas

country: Brazil

institute: UFABC - Universidade Federal do ABC

description: This hybridization is part of an experiment aimed at performing comparative genomic analyses among different isolates of Xylella fastidiosa

hyb_protocol: Labelled DNAs were mixed, dried in a Savant speed vacuum and resuspended in 100 ul of 1X Hybridization buffer, containing 6X SSC, 5X Denhardts solution, 0,25 mg/ml salmon sperm DNA, 0,01% SDS´and 50% formamide. Arrays were hybridized overnight (42oC) in a Gene-Tac Hybridization Station (Genomic Solutions, Inc., Ann Arbor, MI) and washed twice (42oC) in 0.5 X SSC, 0.01 % SDS, followed by two washes in 0.06 X SSC, 0.01 % SDS and two final washes in 0.06 X SSC. All washing steps consisted of 1 min of flow, followed by 5 min of incubation. Slides were then dried and subjected to fluorescent detection

scan_protocol: Slides were subjected to fluorescent detection with a GMS (Affymetrix) 418 Array Scanner (Affymetrix Inc., Santa Clara, CA) Cy3 channel was scanned at 100% laser power and 80% PMT gain Cy5 channel was scanned at 100% laser power and 80% PMT gain

data_processing: Hybridized arrays were scanned in an Affymetrix 418 Array Scanner and images were analyzed with Affymetrix Jaguar v 2.0. Quality control of the hybridized spots was automatically performed by the software, based on spot morphology and local signal-to-background ratio, using the Easy Threshold and Variable Circle Size Algorithms. In all experiments, reliable hybridization signals could be obtained for more than 90% of the arrayed probes. Normalization between the intensities in the two channels was achieved with the Jaguar Control Spots option, using a list of 30 control ORFs that shared sequence identity in the genomes of strains 9a5c and Temecula-1.

molecule: genomic DNA

organism: Xylella fastidiosa

source_name: Xylella fastidiosa 9a5c cells grown in PW medium

label_protocol: DNA labelling was performed as described by: Behr, M.A., Wilson, M.A., Gill, W.P., Salamon, H., Schoolnik, G.K., Rane, S. and Small, P.M. (1999) Comparative genomics of BCG vaccines by whole-genome DNA Microarray. Science 284, 1520-1523.

growth_protocol: Bacteria have been recovered from -70oC glycerol stocks and inoculated onto PW agar plates. Plates were maintained for 10 days at 28oC. The colonies were transferred once to new plates containing the same medium, grown for 20 days and harvested for DNA extraction

extract_protocol: Total genomic DNA was extracted according to : Dungan, D. (1989) in: Current Protocols in Molecular Biology (Ausubel, F.M., Brent, R., Kingston, R.E., Moore, D.D., Seidman, J.G., Smith, J.A. and Struhl, K., Eds.), pp. 241-242. John Wiley and Sons, New York.

tag: Total DNA from Xylella fastidiosa (isolate 9a5c), grown on solid PW medium

source_name: Xylella fastidiosa Fb7 cells grown in PW medium

tag: Total DNA from Xylella fastidiosa (isolate Fb7), grown on solid PW medium


title: Gene expression of mouse ES cell, control of Dnmt1 KO

status: Public on Feb 21 2008

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

description: The Polycomb group (PcG) gene products mediate heritable silencing of developmental regulators in metazoans, participating in one of two distinct multimeric protein complexes, the Polycomb repressive complexes-1 (PRC1) and -2 (PRC2)1-5.  PRC2 catalyses trimethylation of histone H3 at lysine 27 (H3K27) which in turn is thought to provide a recruitment site for PRC13-7. Recent studies demonstrate that mono-ubiquitylation of histone H2A at lysine 119 is important in PcG mediated silencing with the core PRC1 component Ring1A/B functioning as the E3 ligase8.  PRC2 has been shown to share target genes with the core transcription network to maintain embryonic stem (ES) cells including Oct4 and Nanog9. Here we identify an essential role for PRC1 in repressing developmental regulators in ES cells, and thereby in maintaining ES cell pluripotency. A significant proportion of the PRC1 target genes are also repressed by Oct4.  We demonstrate that engagement of PRC1 and PRC2 at target genes is Oct4-dependent and moreover that Ring1B interacts with Oct4. Collectively these results show that PcG complexes are instrumental in Oct4-dependent repression required to maintain pluripotency of ES cells. This study provides a first functional link between a core ES cell regulator and global epigenetic regulation of the genome.

hyb_protocol: 20 micrograms of labeled target RNA was hybridized with Mouse Genome 430 2.0 GeneChip expression arrays (Affymetrix) at 45°C for 16 h, as described in the manufacturer's instructions. Washing stages and streptavidin-phycoerythrin staining were conducted using a GeneChip Fluidics Station (Affymetrix).

scan_protocol: The GeneChips were scanned using GeneChip Scanner 3000 (Affymetrix).

data_processing: MAS5 [the standard algorhithm provided by Affymetrix (http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf)]

source_name: Mus musculus embryonic stem cells, control of Dnmt1 KO

label_protocol: cDNA synthesis, cRNA amplification, biotinylation and fragmentation were performed with a One-Cycle Target Labeling Kit (Affymetrix).

extract_protocol: Total RNA was extracted using the Trizol reagent (Invitrogen) and purified with Qiagen RNeasy separation columns (Qiagen).

tag: Embryonic stem cells, Strain; 129/B6 hybrid


title: Terbutyl stress TR t41 replicate 1

source_name: W303-1a strain replicate 1 growing in exponential phase

tag: In vivo labeled total RNA from W303-1a yeast strain.

tag: Hybridization on macrochip F9.


title: WT_Glu_Air_7.60_Generations_Rep_2

status: Public on Jun 30 2006

first: Kurt

middle: E

last: Kwast

address: 407 S. Goodwin Ave.

department: Molecular & Integrative Physiology

institute: University of Illinois at Urbana-Champaign

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on glucose medium (SSD-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 for 6 generations of anaerobic growth. After six generations, the saprge gas was switched back to air and samples were harvested at 7.60 generations.  30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5)under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Glu_Air_7.60_Generations_Rep_3


title: Normal control skin epithelium_8

hyb_protocol: 3DNA array detection 350 kit (Genisphere)

source_name: universal human reference RNA (Stratagene, Cedar Creek, TX)


title: Normal control skin epithelium_5

extract_protocol: universal human reference RNA (Stratagene, Cedar Creek, TX)


title: Basal cell carcinoma_nodular_1

source_name: basal cell carcinoma_nodular

tag: basal cell carcinoma_nodular

treatment_protocol: universal human reference RNA (Stratagene, Cedar Creek, TX)


title: Gene expression of mouse ES cells, Dnmt1 KO


title: Basal cell carcinoma_nodular_5


title: Basal cell carcinoma_nodular_6


title: Basal cell carcinoma_nodular_2


title: Normal control skin epithelium_1


title: Basal cell carcinoma_nodular_3


title: Normal control skin epithelium_3


title: Basal cell carcinoma_nodular_7


title: Normal control skin epithelium_6


title: Basal cell carcinoma_nodular_4


title: Normal control skin epithelium_2


title: ChIP-chip experiment of mouse ES cells using Ring1B antibody, 1 of 2

status: Public on Feb 16 2008

hyb_protocol: Labeled DNA were hybridized to the Mouse Promoter ChIP-on-chip Microarrays (G4490A, Agilent) for 40 hours at 65 degrees C. The arrays were washed according to the Agilent mammalian ChIP-on-chip protocol (Version 9.0, August 2006).

scan_protocol: Hybridized arrays were scanned with the Agilent G2505B Scanner according to the Agilent mammalian ChIP-on-chip protocol (Version 9.0, August 2006).

data_processing: Scanned images were quantified with Agilent Feature Extraction software under standard conditions (Agilent mammalian ChIP-on-chip protocol version 9.0)

label_protocol: IP DNA and WCE DNA were labeled with Cy5 and Cy3, respectively, using Invitrogen’s CGH labeling kit according to the Agilent mammalian ChIP-on-chip protocol (Version 9.0, August 2006).

extract_protocol: ChIP on chip analysis of Ring1B binding was carried out using the Mouse Promoter ChIP-on-chip Microarray Set (G4490A, Agilent, Palo Alto, Calif., USA). ES cells were subjected to ChIP assay using anti-Ring1B monoclonal antibody as described (Fujimura et al. 2006). Purified immunoprecipitated and input DNA was subjected to blunt ligation with linker oligo DNA, linker mediated PCR (LM-PCR), labeling, hybridization and washing following Agilent mammalian ChIP-on-chip protocol (Version 9.0, August 2006).


title: MCF-7aro Control 3

source_name: MCF7-aro parental control replicate 3


title: Normal control skin epithelium_4


title: WT_Glu_Air_6.80_Generations_Rep_2

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on glucose medium (SSD-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 for 6 generations of anaerobic growth. After six generations, the saprge gas was switched back to air and samples were harvested at 6.80 generations.  30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5)under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Glu_Air_6.80_Generations_Rep_1


title: WT_Glu_Air_6.60_Generations_Rep_3

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on glucose medium (SSD-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 for 6 generations of anaerobic growth. After six generations, the saprge gas was switched back to air and samples were harvested at 6.60 generations.  30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5)under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Glu_Air_6.80_Generations_Rep_3


title: WT_Glu_Air_6.40_Generations_Rep_1

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on glucose medium (SSD-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 for 6 generations of anaerobic growth. After six generations, the saprge gas was switched back to air and samples were harvested at 6.40 generations.  30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5)under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Glu_Air_6.40_Generations_Rep_2


title: WT_Glu_Air_7.60_Generations_Rep_1


title: WT_Glu_Air_6.60_Generations_Rep_2


title: Testosterone + letrozole T+LET 2

source_name: Testosterone + Letrozole Resistant, replicate 2


title: WT_Glu_Air_6.20_Generations_Rep_2

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on glucose medium (SSD-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 for 6 generations of anaerobic growth. After six generations, the saprge gas was switched back to air and samples were harvested at 6.20 generations.  30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5)under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: Testosterone T-only 3

source_name: Testosterone-Only, replicate 3


title: WT_Glu_Air_6.20_Generations_Rep_3


title: WT_Glu_Air_6.30_Generations_Rep_1

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on glucose medium (SSD-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 for 6 generations of anaerobic growth. After six generations, the saprge gas was switched back to air and samples were harvested at 6.30 generations.  30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5)under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Glu_Air_6.30_Generations_Rep_3


title: WT_Glu_Air_6.60_Generations_Rep_1


title: WT_Glu_Air_6.20_Generations_Rep_1


title: WT_Glu_Air_6.30_Generations_Rep_2


title: Basal cell carcinoma_nodular_8


title: WT_Glu_Air_6.13_Generations_Rep_3

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on glucose medium (SSD-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 for 6 generations of anaerobic growth. After six generations, the saprge gas was switched back to air and samples were harvested at 6.13 generations.  30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5)under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Glu_Air_6.13_Generations_Rep_1


title: WT_Glu_Air_6.13_Generations_Rep_2


title: WT_Glu_Air_6.10_Generations_Rep_3

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on glucose medium (SSD-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 for 6 generations of anaerobic growth. After six generations, the saprge gas was switched back to air and samples were harvested at 6.10 generations.  30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5)under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Glu_Air_6.40_Generations_Rep_3


title: WT_Glu_Air_6.10_Generations_Rep_2


title: WT_Glu_Air_6.10_Generations_Rep_1


title: ChIP-chip experiment of mouse ES cells using Ring1B antibody, 2 of 2


title: WT_Glu_Air_6.06_Generations_Rep_1

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on glucose medium (SSD-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 for 6 generations of anaerobic growth. After six generations, the saprge gas was switched back to air and samples were harvested at 6.06 generations.  30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5)under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Glu_Air_6.0_Generations_Rep_3

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on glucose medium (SSD-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 for 6 generations of anaerobic growth. After six generations, the saprge gas was switched back to air and samples were harvested at 6 generations (anaerobic control).  30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5)under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Glu_N2_6_Generations_Rep_2

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on glucose medium (SSD-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 and samples were harvested at 6 generations of anaerobic growth. 30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5) under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Glu_Air_6.03_Generations_Rep_1

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on glucose medium (SSD-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 for 6 generations of anaerobic growth. After six generations, the saprge gas was switched back to air and samples were harvested at 6.03 generations.  30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5)under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Glu_Air_6.03_Generations_Rep_3


title: WT_Glu_Air_6.06_Generations_Rep_2


title: WT_Glu_Air_6.06_Generations_Rep_3


title: WT_Glu_N2_6_Generations_Rep_3


title: WT_Glu_Air_6.0_Generations_Rep_1


title: WT_Glu_N2_6_Generations_Rep_1


title: WT_Glu_N2_5_Generations_Rep_3

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on glucose medium (SSD-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 and samples were harvested at 5 generations of anaerobic growth. 30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5) under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Glu_N2_3_Generations_Rep_3

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on glucose medium (SSD-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 and samples were harvested at 3 generations of anaerobic growth. 30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5) under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Glu_N2_3_Generations_Rep_2


title: WT_Glu_N2_0.5_Generations_Rep_3

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on glucose medium (SSD-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 and samples were harvested at 0.5 generations of anaerobic growth. 30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5) under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Glu_N2_3_Generations_Rep_1


title: WT_Glu_N2_0.5_Generations_Rep_2


title: WT_Glu_N2_5_Generations_Rep_1


title: WT_Glu_N2_0.5_Generations_Rep_1


title: WT_Glu_N2_4_Generations_Rep_3

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on glucose medium (SSD-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 and samples were harvested at 4 generations of anaerobic growth. 30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5) under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Glu_N2_5_Generations_Rep_2


title: WT_Glu_N2_1_Generation_Rep_3

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on glucose medium (SSD-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 and samples were harvested at 1 generation of anaerobic growth. 30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5) under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Glu_N2_4_Generations_Rep_1


title: WT_Glu_N2_4_Generations_Rep_2


title: WT_Glu_N2_1_Generation_Rep_1


title: WT_Glu_Air_6.0_Generations_Rep_2


title: WT_Glu_N2_0.38_Generations_Rep_3

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on glucose medium (SSD-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 and samples were harvested at 0.38 generations of anaerobic growth. 30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5) under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Glu_N2_1_Generation_Rep_2


title: WT_Glu_N2_0.38_Generations_Rep_2


title: WT_Glu_N2_0.25_Generations_Rep_1

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on glucose medium (SSD-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 and samples were harvested at 0.25 generations of anaerobic growth. 30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5) under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Glu_N2_0.13_Generations_Rep_2

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on glucose medium (SSD-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 and samples were harvested at 0.13 generations of anaerobic growth. 30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5) under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Glu_N2_0.13_Generations_Rep_3


title: WT_Glu_N2_0.25_Generations_Rep_3


title: WT_Glu_N2_0.13_Generations_Rep_1


title: WT_Gal_Air_7.6_Generations_Rep_2

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on galactose medium (SSG-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 for 6 generations of anaerobic growth. After six generations, the saprge gas was switched back to air and samples were harvested at 7.6 generations.  30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5)under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Gal_Air_6.6_Generations_Rep_3

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on galactose medium (SSG-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 for 6 generations of anaerobic growth. After six generations, the saprge gas was switched back to air and samples were harvested at 6.6 generations.  30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5)under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Gal_Air_6.4_Generations_Rep_3

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on galactose medium (SSG-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 for 6 generations of anaerobic growth. After six generations, the saprge gas was switched back to air and samples were harvested at 6.4 generations.  30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5)under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Gal_Air_6.6_Generations_Rep_2


title: WT_Gal_Air_7.6_Generations_Rep_3


title: WT_Gal_Air_7.6_Generations_Rep_1


title: WT_Gal_Air_6.3_Generations_Rep_1

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on galactose medium (SSG-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 for 6 generations of anaerobic growth. After six generations, the saprge gas was switched back to air and samples were harvested at 6.3 generations.  30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5)under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Gal_Air_6.3_Generations_Rep_2


title: WT_Gal_Air_6.8_Generations_Rep_3

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on galactose medium (SSG-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 for 6 generations of anaerobic growth. After six generations, the saprge gas was switched back to air and samples were harvested at 6.8 generations.  30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5)under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Gal_Air_6.8_Generations_Rep_1


title: WT_Gal_Air_6.4_Generations_Rep_2


title: WT_Gal_Air_6.4_Generations_Rep_1


title: WT_Gal_Air_6.2_Generations_Rep_2

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on galactose medium (SSG-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 for 6 generations of anaerobic growth. After six generations, the saprge gas was switched back to air and samples were harvested at 6.2 generations.  30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5)under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Gal_Air_6.2_Generations_Rep_3


title: WT_Gal_Air_6.6_Generations_Rep_1


title: WT_Glu_N2_0.25_Generations_Rep_2


title: WT_Gal_Air_6.2_Generations_Rep_1


title: WT_Gal_Air_6.8_Generations_Rep_2


title: WT_Gal_Air_6.13_Generations_Rep_3

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on galactose medium (SSG-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 for 6 generations of anaerobic growth. After six generations, the saprge gas was switched back to air and samples were harvested at 6.13 generations.  30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5)under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Gal_Air_6.1_Generations_Rep_3

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on galactose medium (SSG-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 for 6 generations of anaerobic growth. After six generations, the saprge gas was switched back to air and samples were harvested at 6.1 generations.  30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5)under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Gal_Air_6.13_Generations_Rep_1


title: WT_Gal_Air_6.1_Generations_Rep_2


title: WT_Gal_Air_6.13_Generations_Rep_2


title: WT_Gal_Air_6.1_Generations_Rep_1


title: WT_Gal_Air_6.03_Generations_Rep_3

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on galactose medium (SSG-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 for 6 generations of anaerobic growth. After six generations, the saprge gas was switched back to air and samples were harvested at 6.03 generations.  30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5)under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Gal_Air_6.06_Generations_Rep_1

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on galactose medium (SSG-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 for 6 generations of anaerobic growth. After six generations, the saprge gas was switched back to air and samples were harvested at 6.06 generations.  30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5)under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Gal_Air_6.0_Generations_Rep_2

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on galactose medium (SSG-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 for 6 generations of anaerobic growth. After six generations, the saprge gas was switched back to air and samples were harvested at 6 (anaerobic control) generations.  30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5)under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Gal_Air_6.03_Generations_Rep_1


title: WT_Gal_Air_6.06_Generations_Rep_3


title: WT_Gal_Air_6.0_Generations_Rep_1


title: WT_Gal_N2_6.0_Generations_Rep_1

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on galactose medium (SSG-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 and samples were harvested at 6 generations of anaerobic growth. 30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5) under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Gal_N2_5.0_Generations_Rep_1

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on galactose medium (SSG-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 and samples were harvested at 5 generations of anaerobic growth. 30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5) under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Gal_N2_5.0_Generations_Rep_2


title: WT_Gal_N2_4.0_Generations_Rep_1

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on galactose medium (SSG-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 and samples were harvested at 4 generations of anaerobic growth. 30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5) under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Gal_Air_6.0_Generations_Rep_3


title: WT_Gal_Air_6.03_Generations_Rep_2


title: WT_Gal_N2_3.0_Generations_Rep_3

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on galactose medium (SSG-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 and samples were harvested at 3 generations of anaerobic growth. 30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5) under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Gal_Air_6.06_Generations_Rep_2


title: WT_Gal_N2_6.0_Generations_Rep_2


title: WT_Gal_N2_5.0_Generations_Rep_3


title: WT_Gal_N2_3.0_Generations_Rep_2


title: WT_Gal_N2_1.0_Generations_Rep_3

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on galactose medium (SSG-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 and samples were harvested at 1 generation of anaerobic growth. 30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5) under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Gal_N2_3.0_Generations_Rep_1


title: WT_Gal_N2_1.0_Generations_Rep_1


title: WT_Gal_N2_4.0_Generations_Rep_2


title: WT_Gal_N2_4.0_Generations_Rep_3


title: WT_Gal_N2_6.0_Generations_Rep_3


title: WT_Gal_N2_0.5_Generations_Rep_3

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on galactose medium (SSG-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 and samples were harvested at 0.5 generations of anaerobic growth. 30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5) under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Gal_N2_0.38_Generations_Rep_3

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on galactose medium (SSG-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 and samples were harvested at 0.38 generations of anaerobic growth. 30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5) under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: Prenodule versus internodes HopT0T15d rep 2

status: Public on Sep 01 2008

city: Lisboa

first: Ana

middle: Margarida

last: Fortes

address: Campus da FCUL

department: Plant Biology

country: Portugal

description: Biological replicate 2 of 3. Comparison of prenodules to internodes at beginning of culture. Both files coming from Versarray and edited for GEPAS are presented

hyb_protocol: The hybridization mix consisted of 30μl of labeled cDNAs, 7,5μg Cot-1 DNA (Invitrogen), 15μg Poly (A+), 7,5μg of salmon sperm DNA, 1.5μl of 50X Denhard´t solution, 7.9μl 20X SSC and 1.5μl 10% SDS (w/v). Mixture was denatured at 97ºC for 2 min, put on ice and then 1μl of 10x DIG blocking (Roche Diagnostic GmbH, Mannheim, Germany) buffer was added. Hybridization was carried out at 65º C in chambers ArrayIt (Telechem International).

scan_protocol: Slides were scanned using VersArray ChipReader® and spot and background intensities quantified using Versarray Analyser software (Bio-Rad).

data_processing: Data files were imported into GEPAS (http://gepas.bioinfo.cipf.es) and log2-transformed prior to normalization (DNMAD). Print-tip Lowess was used for within-slide normalization considering background subtraction. Impute missing values (median). Patterns with less than 70% removed.

organism: Humulus lupulus

source_name: In vitro culture of hop internodes which developed into prenodules, day 15

label_protocol: 70  µg of RNA  was used for cDNA synthesis with a RT primer (oligo dT) for labeling with either Cy3 or Cy5 dye molecules (Amersham, Buckinghamshire, UK) and Revert Aid Hminus Reverse Transcriptase (Fermentas)

growth_protocol: Internodes were kept in vitro on MS medium with IAA, BAP and sucrose

extract_protocol: Total RNA was isolated essentially as described by Rerie et al. (1991, Mol Gen Genet) using phenol/chloroform

treatment_protocol: RNA was extracted from internodes and from material at various morphogenic stages (prenodule, nodule and incipient nodules)

tag: Age

value: day 15

source_name: In vitro culture of hop internodes, day 0

value: day 0 ( at beginning of culture)


title: WT_Gal_N2_0.5_Generations_Rep_1


title: WT_Gal_N2_0.5_Generations_Rep_2


title: WT_Gal_N2_0.38_Generations_Rep_2


title: WT_Gal_N2_1.0_Generations_Rep_2


title: WT_Gal_N2_0.13_Generations_Rep_1

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on galactose medium (SSG-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 and samples were harvested at 0.13 generations of anaerobic growth. 30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5) under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Gal_N2_0.25_Generations_Rep_3

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on galactose medium (SSG-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 and samples were harvested at 0.25 generations of anaerobic growth. 30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5) under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Gal_N2_0.13_Generations_Rep_3


title: WT_Gal_N2_0.25_Generations_Rep_2


title: WT_Gal_N2_0.13_Generations_Rep_2


title: WT_Gal_N2_0.38_Generations_Rep_1


title: WT_Gal_N2_0.25_Generations_Rep_1


title: Patient ID# V23

status: Public on Jun 16 2006

city: Stanford

first: Jacob

middle: M

last: Zahn

address: 279 Campus Dr.

department: Developmental Biology

institute: Stanford University

description: Gene expression data from human skeletal muscle samples.

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on Affymetrix HU-133 2.0 GeneChip array.

scan_protocol: Scanned as indicated in Affymetrix protocol

data_processing: The data were analyzed and normalized using Dchip.  The expression model was positive probe only (PM only).  No lower cutoff was used.

source_name: Skeletal muscle taken from other anatomical region: NON-rectus abdominis

label_protocol: Biotinylated cRNA were prepared from 8 microg total RNA (Protocol at http://cmgm.stanford.edu/~kimlab/aging_muscle).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Muscle samples were surgically removed from patients, snap-frozen immediately after extraction in liquid nitrogen, and stored at -80C until total RNA extraction.

tag: Sex

value: Female


title: Patient ID# V30

scan_protocol: Scanned as indicated in Affymetrix protocol.


title: Patient ID# V12


title: Patient ID# V28

value: Male


title: Patient ID# V13


title: Patient ID# V18


title: Patient ID# V11


title: Patient ID# V17


title: Patient ID# V15


title: Patient ID# V19


title: Patient ID# V22


title: Patient ID# V10


title: Patient ID# V9


title: Patient ID# V7


title: Patient ID# V5


title: Patient ID# V2


title: Patient ID# V4


title: WT_Glu_N2_2_Generations_Rep_3

status: Public on Feb 28 2005

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on glucose medium (SSD-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 and samples were harvested at 2 generations of anaerobic growth. 30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5) under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: J1 ES 0 hr 1, chip MOE430B

status: Public on Dec 06 2005

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

institute: Ottawa Hospital Research Institute

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E201
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=201
SCGP Sample ID:				S242
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=201#SAMPLE_209
Short description:			0 hours of an 11-point time course study on differentiating embryoid bodies from a murine J1 embryonic stem cell line. The time course includes 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 4 days, 7 days, 9 days and 14 days.
Estimated purity:				100%
RNA concentration:			2.0 ug/uL
Num cells for RNA prep:			Undetermined
Sample volume:				15 uL

hyb_protocol: Following fragmentation, cRNA was hybridized on the GeneChip Array and the GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the standard Affymetrix protocol (Expression Analysis Technical Manual Rev. 2, 2005-2006, Affymetrix).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 3000 7G scanner.

data_processing: Calculated using the MAS5 algorithm where sc=1500, tau=0.015, alpha1=0.04, and alpla2=0.06

source_name: J1, Fetal cells

label_protocol: Biotinylated cRNA was prepared from the total RNA according to the Affymetrix protocol (Expression Analysis Technical Manual Rev. 2, 2005-2006, Affymetrix)

growth_protocol:
Growth medium:				ES Cell Medium - DMEM (high glucose)
Media supplements:			Hyclone FCS, non-essential amino acids, Glutamax, Penicillin/Streptomycin, sodium pyruvate, beta-mercaptoethanol, LIF
Culture conditions:			37 C, 5% CO2

extract_protocol:
RNA prep method:				RNeasy
Cell purification method:			Culturing
Contaminating cell type:			None
Method for estimating purity:		By eye

treatment_protocol: Assays to confirm viability:		Stratagene mycoplasma PCR test

tag: Strain:					129/Sv

tag: Gender:					Male


title: RHE2_T5_R3, 24 hr recovery

status: Public on Aug 01 2005

city: Blacksburg

first: Richard

middle: F.

last: Helm

state: VA

address: West Campus Drive

department: Biochemistry, Fralin Biotechnology Center

institute: Virginia Polytechnic Institute and State University

description:
60-70% confluent Human embryonic kidney cell were split into suspension overagarose to form spheroids and grown for an additional 4 days insuspension over agarose prepared with 10% FBS supplemented DMEM
Following growth, media was removed and the spheroids were stored on thesurface of the agarose in vacuum sealed flasks for a 2 week interval at roomtemperature in the dark.
The samples were compared against unstored controls of both spheroids andmonolayer (at 60-70% confluence)samples. All samples were conducted intriplicate.
Rehydration was conducted with DMEM (Invitrogen) containing 10%FBS up tothe final 72hr rehydration timepoint.

source_name: Kidney 293 HEK Cells


title: RHE2_T6_R3, 72 hr recovery


title: RHE2_T6_R1, 72 hr recovery


title: RHE2_T5_R1, 24 hr recovery


title: RHE2_T6_R2, 72 hr recovery


title: RHE2_T4_R2, 6 hr recovery


title: RHE2_T5_R2, 24 hr recovery


title: WT_Glu_N2_0.19_Generations_Rep_3

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on glucose medium (SSD-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 and samples were harvested at 0.19 generations of anaerobic growth. 30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5) under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Glu_N2_0.19_Generations_Rep_2


title: RHE2_T3_R3, 0 hr recovery


title: RHE2_T2_R2, Spheroid prior to storage


title: WT_Glu_N2_2_Generations_Rep_2


title: WT_Glu_N2_0.19_Generations_Rep_1


title: RHE2_T4_R3, 6 hr recovery


title: RHE2_T2_R3, Spheroid prior to storage


title: WT_Glu_N2_2_Generations_Rep_1


title: RHE2_T1_R1, Control Monolayer


title: RHE2_T1_R2, Control Monolayer


title: RHE2_T2_R1, Spheroid prior to storage


title: RHE2_T3_R2, 0 hr recovery


title: RHE2_T3_R1, 0 hr recovery


title: RHE2_T4_R1, 6 hr recovery


title: RHE2_T1_R3, Control Monolayer


title: WT_Glu_N2_0.08_Generations_Rep_3

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on glucose medium (SSD-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 and samples were harvested at 0.08 generations of anaerobic growth. 30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5) under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Glu_N2_0.08_Generations_Rep_2


title: WT_Glu_N2_0.08_Generations_Rep_1


title: WT_Glu_N2_0.04_Generations_Rep_3

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on glucose medium (SSD-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 and samples were harvested at 0.04 generations of anaerobic growth. 30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5) under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Glu_N2_0.04_Generations_Rep_2


title: WT_Glu_N2_0.04_Generations_Rep_1


title: WT_Glu_N2_0_Generations_Rep_2

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on glucose medium (SSD-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 and samples were harvested at 0 generations of anaerobic growth. 30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5) under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Gal_N2_2.0_Generations_Rep_3

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on galactose medium (SSG-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 and samples were harvested at 2 generations of anaerobic growth. 30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5) under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Gal_N2_2.0_Generations_Rep_1


title: WT_Gal_N2_0.08_Generations_Rep_3

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on galactose medium (SSG-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 and samples were harvested at 0.08 generations of anaerobic growth. 30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5) under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Gal_N2_0.19_Generations_Rep_2

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on galactose medium (SSG-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 and samples were harvested at 0.19 generations of anaerobic growth. 30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5) under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Gal_N2_2.0_Generations_Rep_2


title: WT_Gal_N2_0.08_Generations_Rep_1


title: WT_Gal_N2_0.04_Generations_Rep_3

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on galactose medium (SSG-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 and samples were harvested at 0.04 generations of anaerobic growth. 30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5) under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Gal_N2_0.04_Generations_Rep_2


title: WT_Gal_N2_0.19_Generations_Rep_1


title: msn2/4_Galactose_2_Generations_Replicate_3

description: Sparged, fermentor clutures of the msn2/4 mutant strain were aerobically grown on galactose medium (SSG-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 and samples were harvested after 0 (aerobic control), 0.04, 0.08, 0.19, and 2 generations of anaerobic growth.  30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5), which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Gal_N2_0_Generations_Rep_2

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on galactose medium (SSG-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 and samples were harvested at 0 generations of anaerobic growth. 30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5) under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: WT_Gal_N2_0_Generations_Rep_3


title: WT_Glu_N2_0_Generations_Rep_1


title: WT_Gal_N2_0.08_Generations_Rep_2


title: WT_Glu_N2_0_Generations_Rep_3


title: msn2/4_Galactose_2_Generations_Replicate_1


title: WT_Gal_N2_0.04_Generations_Rep_1


title: msn2/4_Galactose_0.19_Generations_Replicate_2


title: msn2/4_Galactose_0.19_Generations_Replicate_3


title: msn2/4_Galactose_2_Generations_Replicate_2


title: WT_Gal_N2_0.19_Generations_Rep_3


title: msn2/4_Galactose_0.19_Generations_Replicate_1


title: msn2/4_Galactose_0.08_Generations_Replicate_3


title: WT_Gal_Air_6.3_Generations_Rep_3

description: Sparged, fermentor clutures of a yeast strain (JM43) were aerobically grown on galactose medium (SSG-TEA).  At time zero (generation 0) the saprge gas was switched from air to O2-free N2 for 6 generations of anaerobic growth. After six generations, the saprge gas was switched back to air and samples were harvested at 6.3 generations.  30 µg of total RNA was reverse transcribed  (Cy3) and hybridized against a reference (Cy5)under the same gas condition, which consisted of a pool of equal masses of RNA from each time point sampled.  The data are background-corrected and normalized.


title: msn2/4_Galactose_0.04_Generations_Replicate_2


title: msn2/4_Galactose_0_Generation_Replicate_1


title: msn2/4_Galactose_0.04_Generations_Replicate_1


title: msn2/4_Galactose_0.04_Generations_Replicate_3


title: msn2/4_Galactose_0_Generation_Replicate_3


title: msn2/4_Galactose_0_Generation_Replicate_2


title: msn2/4_Galactose_0.08_Generations_Replicate_1


title: msn2/4_Galactose_0.08_Generations_Replicate_2


title: WT_Gal_N2_0_Generations_Rep_1


title: Patient ID# V6


title: sys42A 111402.txt~Florence - SYS

status: Public on Aug 11 2008

city: Dallas

first: Damien

last: Chaussabel

state: TX

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

description: A male subject diagnosed with JIA Systemic Onset where age 11 yrs, when sample taken.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 System.

source_name: sys42A 111402, Florence - SYS

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: RNeasy Mini

value: 11 yrs, when sample taken.

tag: Gender

value: M

tag: Ethnicity

value: Not Hispanic or Latino

tag: Race

value: White

tag: Illness

value: JIA Systemic Onset


title: Follicular lymphoma, diagnostic biopsy: 54023

status: Public on Aug 09 2008

first: K-John

last: Cheung

address: 600 West 10th Ave

institute: British Columbia Cancer Agency

description: Follicular lymphoma, diagnostic biopsy

hyb_protocol: Probe pre-hybridization Denature the probe at 85ºC for 10 minutes Allow the Cot-1 DNA to anneal to the DNA probe for 1 hour at 45ºC. Hybridization Maintain the probe at 45ºC. (If necessary pulse-spin the tube to pool any condensed probe.) Pipet 43 ul of the probe solution onto a 24 x 60 mm coverslip prewarmed to 45ºC. Gently lower the slide over the coverslip (try to avoid generating bubbles). Place the slide into a hybridisation cassette. Add 10 ul water into the lower groove of the cassette. Close the hybridization cassette ensuring a good seal is made by the gasket. Incubate for 36-40 hours at 45ºC. Washing Prewarm the wash buffer (0.1 xSSC with 0.1% SDS) to 45ºC. Remove the slide from the hybridization cassette. Soak slide in wash buffer until the coverslip slides off (usually 2-5 minutes). Transfer slide immediately into a fresh coplin jar containing wash buffer. Wash the slide in wash buffer for 5 minutes with agitation. Quickly change the wash buffer and repeat the wash step another 2 times. Rinse the slide with 3 changes of 0.1 x SSC at room temperature, leaving the slide in the final 0.1x SSC so it will not dry out. Dry the slide with a filtered air stream, or centrifuge the slide in a clean, dust-free 50 ml Falcon tube at 700 g for 3 minutes. Store the slides in a dark, dust free box until ready to scan. (If the slides are not scanned within 2 hours, vacuum seal the slide box and leave the box at room temperature until scanning will take place.

scan_protocol: Images were scanned using and API Arrayworx e Auto Scanner. Data was processed using the Softworx (API) analysis package. An Applied Precision Arrayworx CCD scanner is used to scan slides at a 9.75 um resolution and at a high signal to noise ratio (SNR). The exposure time for each image wavelength is between 0.2-2 seconds, the standard exposure time is 1.00 sec for Cy3 and 2.00 sec for Cy5.

data_processing: Data was normalized using the application described in Khojasteh et al BMC Bioinformatics 2005;6:274

label: Cyanine 5

source_name: Follicular lymphoma, diagnostic biopsy

label_protocol: cy3/cy5 labeling

extract_protocol: Genomic DNA extracted by standard ProtK extraction.

tag: tumor grade

value: Tumor grade 1

tag: Overall survival from diagnosis (year)

tag: Time to transformation from diagnosis (year)

label: Cyanine 3

source_name: Normal genomic

tag: Novagen female Genomic DNA